Update: Lara Logan and her producer are taking a leave of absence from "60 Minutes," the network announced Nov. 26, after questions about the Benghazi report detailed below.

When “60 Minutes” apologized for featuring in its report on Benghazi a security contractor whose story turned out to be a lie, it said it had been “misled.” But a close examination of the controversial piece by McClatchy shows that there are other problems with the report, whose broadcast renewed debate about one of the most contentious events in recent U.S. diplomatic history.

In an email Wednesday, CBS declined to respond to questions about the accuracy and origin of some of the other aspects of the report. But it said that it was undertaking “a journalistic review that is ongoing” – the network’s first acknowledgement that concerns about the report may go deeper than just the discredited interview with security supervisor Dylan Davies.

“60 Minutes” spokesman Kevin Tedesco said CBS had begun the review “the moment we confirmed there was an issue in our story.” But he declined to elaborate on the investigation and did not respond to specific issues McClatchy raised about the segment, including unsourced assertions that al Qaida was behind the Benghazi attacks and claims about the investigation that the FBI and other experts question or deny outright.

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The “60 Minutes” report, which was narrated by longtime CBS correspondent Lara Logan, was controversial almost from the moment it was broadcast Oct. 27, as could be expected for another rendition of what took place Sept. 11, 2012, when gunmen stormed a U.S. diplomatic compound and set its main building on fire. U.S. Ambassador Christopher Stevens and State Department computer expert Sean Smith, trapped inside, died of smoke inhalation. Hours later, attackers assaulted a CIA compound nearby, killing two security contractors.

Shortly after the segment aired, Sen. Lindsey Graham, R-S.C., who has been a critic of the Obama administration’s response to the Benghazi attacks, announced that he would block all administration appointments until the FBI surrendered to Congress notes of the interviews it had done with survivors.

But the credibility of the report soon came into question. CBS was taken to task for not revealing that Davies, on whose recollections the report was largely based, was the author of a soon-to-be released book published by a CBS-owned publishing company that features the work of politically conservative authors. On Oct. 31, The Washington Post revealed that Davies had filed a report with his employer, Blue Mountain Security, that contradicted his “60 Minutes” account, and The New York Times revealed Nov. 7 that Davies also gave an account to the FBI at odds with the “60 Minutes” version.

After The New York Times story was posted online, CBS quickly purged its websites of any mention of the piece and even demanded that a copy of the segment be removed from YouTube. On Sunday, Logan, in a brief appearance at the end of the regular “60 Minutes” broadcast, acknowledged that Davies had misled her and her crew and that “it was a mistake to include him in our report.”

But Logan’s mea culpa said nothing about other weaknesses in the report that a line-by-line review of the broadcast’s transcript reveals. McClatchy turned to LexisNexis, a legal research service, for a transcript of the broadcast because the segment no longer appeared on CBS sites.

The report repeatedly referred to al Qaida as solely responsible for the attack on the compound and made no mention of Ansar al Shariah, the Islamic extremist group that controls and provides much of the security in restive Benghazi and that has long been suspected in the attack. While the two organizations have worked together in Libya, experts said they have different aims – al Qaida has global objectives while Ansar al Shariah is focused on turning Libya into an Islamic state.

It is an important distinction, experts on those groups said. Additionally, al Qaida’s role, if any, in the attack has not been determined, and Logan’s narration offered no source for her repeated assertion that it had been.

“I think there are definitely connections, but I am not sure there is command and control” between al Qaida and Ansar al Shariah, said Aaron Y. Zelin of the Washington Institute for Near East Policy, who studies insurgent activity in North Africa.

Logan claimed that “it’s now well established that the Americans were attacked by al Qaida in a well-planned assault.” But al Qaida has never claimed responsibility for the attack, and the FBI, which is leading the U.S. investigation, has never named al Qaida as the sole perpetrator. Rather, it is believed a number of groups were part of the assault, including members and supporters of al Qaida and Ansar al Shariah, as well as attackers angered by a video made by an American that insulted Prophet Muhammad. The video spurred angry protests outside the U.S. embassy in Cairo hours beforehand.

In a Sept. 12, 2012, statement about the attack, Ansar al Shariah suggested its members had participated, though the group said it did not order the assault.

Moreover, questions remain over how far in advance the attack on the U.S. compound had been planned. Rather than a long-planned attack, investigators have told McClatchy it was likely planned hours, rather than days, in advance.

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Another questionable assertion in the “60 Minutes” report was Logan’s unsourced reference to the Benghazi Medical Center as being “under the control of al Qaida terrorists,” an assertion that McClatchy correspondents on the ground at the time and subsequent reporting in Benghazi indicates is untrue.

Around midnight, after the attack on the diplomatic compound, looters who descended on the site discovered Stevens in a safe room and took him to the medical center, where a doctor tried to revive him for 45 minutes before pronouncing him dead.

In the “60 Minutes” report, Davies, the discredited security contractor, claimed to have snuck into the hospital, where he saw Stevens, even though the hospital was “under the control of al Qaida terrorists.”

On the night of the attack, the medical center, whose compound includes several buildings in addition to the relatively modern, multi-story hospital itself, was being guarded by Ansar al Shariah. Libyan residents McClatchy spoke with said the group’s guards never stopped patients from entering but were there primarily to protect the nurses and doctors inside.

The Libyan Herald, an English-language news outlet, reported just three days before the diplomatic compound was attacked that the Libyan health minister and the French ambassador to Libya, Antoine Sivan, had visited the facility to break ground on an expansion. Had the hospital been under al Qaida control, it is unlikely doctors could have spent nearly an hour trying save Stevens’ life or that the health minister of the government it seeks to oust would have been allowed to enter the hospital.

The piece also named three known insurgent operators as top suspects in the attack but did not explain the source of that assertion.

The three are long suspected of having been involved, Zelin said, but there is no evidence of their specific roles in the attack.

Two months ago, al Qaida operative Abu Anas al-Libi was captured in Tripoli by U.S. commandoes and brought to New York to stand trial for his alleged role in the 1998 bombing of U.S. embassies in Tanzania and Kenya. The “60 Minutes” piece attempted to link al-Libi to the events in Benghazi, with Logan reporting that “Abu Anas al-Libi was captured for his role in the Africa bombings and the U.S. is still investigating what part he may have played in Benghazi.”

But a U.S. law enforcement source involved in the Benghazi probe, who spoke on the condition of anonymity because he was not authorized to discuss a case that’s still under investigation, told McClatchy this week that al-Libi is not under investigation for the Benghazi attacks. Logan did not detail the source for her assertion that he was.

Another man, Sufain bin Qumu, which the piece describes as an “al Qaida operative,” was a known member of Ansar al Shariah, heading up its operation in the eastern Libyan city of Darna. The piece said he was a “lead partner” in the attack.

But while Qumu, a former Guantanamo Bay detainee, is believed to have worked with al Qaida at times, Zelin said, no evidence has emerged of his role in Benghazi other than a Fox News report last month that he was on the ground in Benghazi the night of the attack. The Fox News piece noted “it is not clear whether Qumu was directing the assault.” Logan offered no source for her claim that he led the attack.

The third man named in the piece is Faraj al-Chalabi. The piece described al-Chalabi as someone “whose ties to Osama bin Laden go back more than 15 years. He’s believed to have carried documents from the compound to the head of al Qaida in Pakistan.”

Libyan authorities detained al-Chalabi in March as a potential witness to the attack but released him in June. U.S. officials at the time said there was not enough evidence to hold him for the Benghazi attack, though questions arose about whether that was because U.S. officials had failed to provide the evidence to Libyan authorities.

If there is new evidence that any of the men were involved, the segment did not detail what it was or how Logan knew about it.

The piece closed with a picture of a document outlining Stevens’ schedule for Sept. 12, “a day (Stevens) did not live to see.” According to the piece, “When a member of our team went to the U.S. compound earlier this month, he found remnants of the Americans’ final frantic moments still scattered on the ground.”

But the compound owner, Jamal el Bishari, told McClatchy on Wednesday that he began clearing debris in April from the compound’s four buildings and is still renovating the site. McClatchy visited the site in June and saw a pile of debris sitting outside the compound walls, but no documents were discernible among the broken concrete, clothing, furniture and soot.

Bishari said it is unlikely such a document could have been discovered recently.

“It is impossible to find a document now,” he told McClatchy.

In “60 Minutes Overtime,” an addendum to the piece that was available online and outlined how CBS spent a year reporting the story, the piece’s producer, Max McClellan, explained how the program obtained the schedule.

“The person who shot this footage has a lot of experience in Libya and through his network of contacts on the ground in Benghazi, he was able to access the compound. It was closed, guarded, but through relatives of people he had gotten to know over the years, he was able to get in and take these pictures for us,” McClellan said. “We did not expect that we would find the U.S. compound in the state that we found it. There was still debris and ammunition boxes and a whiteboard that had the day’s assignment for the security personnel at the compound as of September 11, 2012.”

El Bishari said that he could not remember when he removed the remnants of the attack as part of the renovation, but what McClatchy’s June visit showed was that little debris remained inside the compound then. A local journalist who visited the site in September on assignment for Fox News told McClatchy Tuesday that any documents that remained at the site then would have been inconsequential. He returned to the site Tuesday at McClatchy’s request and took photos, which showed that the debris piles evident in June had been removed.

CBS spokesman Tedesco declined to respond to a specific question of “whether it was a CBS News employee or someone else who went to the site” or “when and how exactly he/she found the document.”

Davies had claimed in the “60 Minutes” piece that he had gone to the diplomatic compound site during the attack, climbed a 12-foot-high wall and struck one of the attackers in the head with his rifle butt before discovering Stevens’ body at the hospital. All of the claims contradicted multiple reports that have emerged in the year since the attacks.

Since “60 Minutes” acknowledgement that Davies had lied in his interviews, CBS also has not explained how Davies came to play such a major role in the segment and what role if any his connection to CBS-owned Threshold Editions had in his prominence. Threshold, which also has published books by former Vice President Dick Cheney, Republican strategist Karl Rove and conservative commentator Glenn Beck, withdrew Davies’ book from circulation last week.

McClatchy special correspondent Dawood Idreesi contributed to this report from Benghazi.